RetrogeneDB ID: retro_mmul_1130

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:128603747..128604179(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BAK1
• Ensembl ID: ENSMMUG00000009104
• Aliases: None
• Description: bcl-2 homologous antagonist/killer [Source:RefSeq peptide;Acc:NP_001253660]

Sequence

>retro_mmul_1130
CCTAGCAGCACCGTGGGGCAGGTGGGATGGCAGATCGCCATCATCTGGGATGACATCAATCGGCGCTATGACTCGGAATT
CTAGACCATGCTGCAGCACCTGCAGCCCACAGCAGAGAACGCCTATGAGTACTTCACCAAGATCGCCTCCAGCCTGTTTG
AGAGTGGCATCAACCAGGGCCGTGTGGTGGCTCTCCTGGGCTTCGGCTACCATCTGGTCCTACATGTCTACCAGCGCGGC
TTGACTGGCTTCCTGGGCCAGGTGACCCGCTTCGTGGTCTTCATGCTGTAACACTGCATCACCTGGTGGATCGCGCAGAG
GAGCAGCTGGGTGGCAGCCCTGGACTTGGGCAATGGTCCCATCCTGAACGTGCTGGTGATTCTGGGGGTGGTTCTGTTGG
GCCTGTTTGTGGTACAAGGATTCTTCAAATCA

Alignment

ORF - retro_mmul_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSSTMGQVGRQLAIIGDDINRRYDSEFQTMLQHLQPTAENAYEYFTKIASSLFESGINWGRVVALLGFGY
          PSST.GQVG.Q.AII.DDINRRYDSEF.TMLQHLQPTAENAYEYFTKIASSLFESGIN.GRVVALLGFGY
Retrocopy PSSTVGQVGWQIAIIWDDINRRYDSEF*TMLQHLQPTAENAYEYFTKIASSLFESGINQGRVVALLGFGY

Parental  RLALHVYQHGLTGFLGQVTRFVVDFMLHHCIARWIAQRGGWVAALNLGNGPILNVLVVLGVVLLGQFVVR
          .L.LHVYQ.GLTGFLGQVTRFVV.FML.HCI..WIAQR..WVAAL.LGNGPILNVLV.LGVVLLG.FVV.
Retrocopy HLVLHVYQRGLTGFLGQVTRFVV-FML*HCITWWIAQRSSWVAALDLGNGPILNVLVILGVVLLGLFVVQ

Parental  RFFKS
          .FFKS
Retrocopy GFFKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	4.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.60 RPM
SRP007412_cerebellum	0.00 RPM	7.49 RPM
SRP007412_heart	0.00 RPM	10.83 RPM
SRP007412_kidney	0.00 RPM	16.20 RPM
SRP007412_liver	0.00 RPM	6.45 RPM
SRP007412_testis	0.00 RPM	4.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1130 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1130 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_942
Pan troglodytes	retro_ptro_652
Gorilla gorilla	retro_ggor_761

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013657	1 retrocopy	retro_fcat_202,
Homo sapiens	ENSG00000030110	2 retrocopies	retro_hsap_2468, retro_hsap_942,
Gorilla gorilla	ENSGGOG00000022462	1 retrocopy	retro_ggor_761,
Macaca mulatta	ENSMMUG00000009104	1 retrocopy	retro_mmul_1130 ,
Nomascus leucogenys	ENSNLEG00000008351	1 retrocopy	retro_nleu_296,
Ochotona princeps	ENSOPRG00000001127	2 retrocopies	retro_opri_105, retro_opri_938,
Pan troglodytes	ENSPTRG00000018053	1 retrocopy	retro_ptro_652,